1. Introduction
MAVEQC is a flexible R-package that provides QC analysis of
Saturation Genome Editing (SGE) experimental data. Available under GPL
3.0 from https://github.com/wtsi-hgi/MAVEQC
2. Screen QC
Displays QC plots and statistics for all samples for QC.
2.2. Run Sample QC
2.2.1. Read Length Distrubtion
Displays the percentage of reads for each sample, based on 50
nucleotide increments.

2.2.2. Missing Variants
Missing variants in the library
2.2.3. Total Reads
Displays the total number of reads per sample. Filtering based on
1-dimensional Kmean clustering that excludes unique sequences with low
read counts.
- Accepted reads: Total read count for all unique
sequences with sufficient reads.
- Excluded reads: Total read count for all unique
sequences with insufficient reads.

2.2.4. Accepted Reads
Displays the percentage of library reads vs non-library reads (ie.
Reference, PAM and Unmapped) for Accepted Reads.
- Library Reads: Percentage reads mapping to template
oligo sequences, including intended variants.
- Reference Reads: Percentage reads mapping to
Reference.
- PAM_Reads: Percentage reads mapping to
PAM/Protospacer Protection Edits (PPEs), without intended variant.
- Unmapped Reads: Percentage of Unmapped Reads.
- Library Coverage: Mean read count per template
oligo sequence.

Defines the mean read count per template oligo sequence.
2.2.5. Genomic Coverage
Distribution of variants across targeton region based on log2(count+1)
values.
Note: missing variants (0 count in the library) are not included.

2.2.6. Genomic Position Percentage
Displays distribution of “LOF” (loss-of-function) vs all “Other”
variants across the targeton region, based on read percentages for
reference timepoint. Requires concordant distribution of LOF and Other
variants.
Note: missing variants (0 count in the library) are not included.

2.3. Run Experiment QC
2.3.1. Sample Correlations

2.3.2. Sample PCA
2.3.3. Fold Change (by category)
condition_D7_vs_D4

condition_D15_vs_D4

2.3.4. Fold Change (by position)
condition_D7_vs_D4

condition_D15_vs_D4

3. QC Results
Summarising the final results, below are the cutoffs using for
PASS/FAIL